What textures/materials do you have in the model? Maybe there is a color lookup change happening between the PDF and jpg that is making some material look more yellow?
To answer your second question, no, jpg does not always look good to me. In particular, unless I have profiles set to 1 they come out very heavy in the jpg. Like Dave, unless I know the recipient can only handle jpg, I prefer png, uncompressed tiff, or PDF.